Effect of the X chromosome in genomic evaluations of reproductive traits in beef cattle

Diaz, Iara Del Pilar Solar; Camargo, Gregório Miguel Ferreira de; Cruz, Valdecy Aparecida Rocha da; Hermisdorff, Isis da Costa; Carvalho,; Albuquerque, Lúcia Galvão de; Costa, Raphael Bermal

doi:10.1016/j.anireprosci.2020.106682

Cited by 3 publications

(1 citation statement)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, SNPs located on the X chromosome tend to be ignored in genomic analyses of complex traits, mainly because of the analytical challenges and biological considerations [ 28 – 30 ]. Recently, the inclusion of the X chromosome in such analyses was suggested to improve the accuracy of genomic prediction in both dairy and beef cattle [ 28 , 31 ]. To the best of our knowledge, SNPs located on the X chromosome have rarely been included in genomic analyses of the pig, especially of G × E interactions based on reproduction traits, and, thus, limited information is available on genomic polymorphisms and functional genes on the X chromosome that are associated with reproduction traits [ 13 , 14 , 32 ].…”

Section: Introductionmentioning

confidence: 99%

Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms

et al. 2021

View full text Add to dashboard Cite

Background There is an increasing need to account for genotype-by-environment (G × E) interactions in livestock breeding programs to improve productivity and animal welfare across environmental and management conditions. This is even more relevant for pigs because selection occurs in high-health nucleus farms, while commercial pigs are raised in more challenging environments. In this study, we used single-step homoscedastic and heteroscedastic genomic reaction norm models (RNM) to evaluate G × E interactions in Large White pigs, including 8686 genotyped animals, for reproduction (total number of piglets born, TNB; total number of piglets born alive, NBA; total number of piglets weaned, NW), growth (weaning weight, WW; off-test weight, OW), and body composition (ultrasound muscle depth, MD; ultrasound backfat thickness, BF) traits. Genetic parameter estimation and single-step genome-wide association studies (ssGWAS) were performed for each trait. Results The average performance of contemporary groups (CG) was estimated and used as environmental gradient in the reaction norm analyses. We found that the need to consider heterogeneous residual variance in RNM models was trait dependent. Based on estimates of variance components of the RNM slope and of genetic correlations across environmental gradients, G × E interactions clearly existed for TNB and NBA, existed for WW but were of smaller magnitude, and were not detected for NW, OW, MD, and BF. Based on estimates of the genetic variance explained by the markers in sliding genomic windows in ssGWAS, several genomic regions were associated with the RNM slope for TNB, NBA, and WW, indicating specific biological mechanisms underlying environmental sensitivity, and dozens of novel candidate genes were identified. Our results also provided strong evidence that the X chromosome contributed to the intercept and slope of RNM for litter size traits in pigs. Conclusions We provide a comprehensive description of G × E interactions in Large White pigs for economically-relevant traits and identified important genomic regions and candidate genes associated with GxE interactions on several autosomes and the X chromosome. Implementation of these findings will contribute to more accurate genomic estimates of breeding values by considering G × E interactions, in order to genetically improve the environmental robustness of maternal-line pigs.

show abstract

Section: Introductionmentioning

confidence: 99%

Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms

et al. 2021

View full text Add to dashboard Cite

show abstract

X-linked genes influence various complex traits in dairy cattle

Sanchez,

Escouflaire,

Baur

et al. 2023

BMC Genomics

View full text Add to dashboard Cite

Background The search for quantitative trait loci (QTL) affecting traits of interest in mammals is frequently limited to autosomes, with the X chromosome excluded because of its hemizygosity in males. This study aimed to assess the importance of the X chromosome in the genetic determinism of 11 complex traits related to milk production, milk composition, mastitis resistance, fertility, and stature in 236,496 cows from three major French dairy breeds (Holstein, Montbéliarde, and Normande) and three breeds of regional importance (Abondance, Tarentaise, and Vosgienne). Results Estimates of the proportions of heritability due to autosomes and X chromosome (h²X) were consistent among breeds. On average over the 11 traits, h²X=0.008 and the X chromosome explained ~ 3.5% of total genetic variance. GWAS was performed within-breed at the sequence level (~ 200,000 genetic variants) and then combined in a meta-analysis. QTL were identified for most breeds and traits analyzed, with the exception of Tarentaise and Vosgienne and two fertility traits. Overall, 3, 74, 59, and 71 QTL were identified in Abondance, Montbéliarde, Normande, and Holstein, respectively, and most were associated with the most-heritable traits (milk traits and stature). The meta-analyses, which assessed a total of 157 QTL for the different traits, highlighted new QTL and refined the positions of some QTL found in the within-breed analyses. Altogether, our analyses identified a number of functional candidate genes, with the most notable being GPC3, MBNL3, HS6ST2, and DMD for dairy traits; TMEM164, ACSL4, ENOX2, HTR2C, AMOT, and IRAK1 for udder health; MAMLD1 and COL4A6 for fertility; and NRK, ESX1, GPR50, GPC3, and GPC4 for stature. Conclusions This study demonstrates the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle and highlights new functional candidate genes and variants for these traits. These results could potentially be extended to other species as many X-linked genes are shared among mammals.

show abstract

Genetic Contributions of Genes on Sex Chromosomes and Mitochondrial DNA in a Pedigreed Population

Ogawa

Satoh

2022

Diversity

View full text Add to dashboard Cite

The genetic contribution with respect to autosomal genes has been widely used to evaluate the genetic diversity of a target population. Here, we developed a method to calculate the genetic contribution with respect to genes on sex chromosomes and mitochondrial DNA through pedigree analysis. To demonstrate the performance, we applied the methods for calculating genetic contributions to example pedigree data. To verify the results of genetic contribution calculations, we performed gene-dropping simulations mimicking flows of genes on autosomes, X and Y chromosomes, and mitochondrial DNA, and then compared the results from the simulation with the corresponding genetic contributions. To investigate the effect of pedigree error, we compared the results of genetic contribution calculations using pedigree data with and without errors. The results of gene-dropping simulation showed good agreement with the results of the genetic contribution calculation. The effect of pedigree errors on the calculation of genetic contribution depended on the error rate. Since the patterns of the genetic contributions of such genes might be different from those on autosomes, the novel approach could provide new information on the genetic composition of populations. The results are expected to contribute to the development of methods for sustainable breeding and population management.

show abstract

Effect of the X chromosome in genomic evaluations of reproductive traits in beef cattle

Cited by 3 publications

References 19 publications

Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms

Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms

X-linked genes influence various complex traits in dairy cattle

Genetic Contributions of Genes on Sex Chromosomes and Mitochondrial DNA in a Pedigreed Population

Contact Info

Product

Resources

About